13-44224061-C-T

Variant names:

• chr13-44224061-C-T
• rs2248414
• ENST00000437867.6:n.1492-14767C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000618753.4(SMIM2-AS1):​n.412-14767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,054 control chromosomes in the GnomAD database, including 7,198 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7198 hom., cov: 32)
• Consequence: SMIM2-AS1 ENST00000618753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 5 publications found

Genes affected

SMIM2-AS1 (HGNC:42674): (SMIM2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000618753.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM2-AS1	ENST00000437867.6	TSL:5	n.1492-14767C>T		intron	N/A
	SMIM2-AS1	ENST00000618753.4	TSL:4	n.412-14767C>T		intron	N/A
	SMIM2-AS1	ENST00000659169.2		n.613-14767C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44995 AN: 151936 Hom.: 7190 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 45024 AN: 152054 Hom.: 7198 Cov.: 32 AF XY: 0.296 AC XY: 21965 AN XY: 74328

African (AFR) AF: 0.168 AC: 6952 AN: 41504

American (AMR) AF: 0.316 AC: 4824 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1531 AN: 5156

South Asian (SAS) AF: 0.288 AC: 1381 AN: 4796

European-Finnish (FIN) AF: 0.337 AC: 3563 AN: 10572

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24501 AN: 67958

Other (OTH) AF: 0.305 AC: 645 AN: 2114

Alfa AF: 0.333 Hom.: 27776

Bravo AF: 0.290

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2248414;

hg19: chr13-44798197;